In brief (and if any legal scholar has additional detail to provide I’d be interested in the answer as well!) Yes, the emancipation proclamation was legal specifically because it was focused on freeing slaves in rebellious states. Note that it did Not free slaves in states within the union (the 13th amendment did that) but was a proclamation that freed enslaved persons in rebelling states if they were to remain in a state of rebellion. Because of this it fell under the executive authority of the president to issue in order to quell rebellion within the United States- as Commander in Chief he had such authority over areas where the US (Union) Army and Navy were active. Lincoln would not have been able to (legally) issue an order freeing slaves in peacetime or in the slaveholding states which weren’t in rebellion, which is why the 13th amendment to the Constitution was later proposed and ratified.